IQ-TREE multicore version 1.6.11 for Linux 64-bit built Jun  6 2019
Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor,
Heiko Schmidt, Dominik Schrempf, Michael Woodhams.

Host:    rabi (SSE4.2, 15 GB RAM)
Command: ../../iqtree -s Troglosironidae_18S.mafft.fasta -m TESTNEW -bb 1000 -alrt 1000
Seed:    382075 (Using SPRNG - Scalable Parallel Random Number Generator)
Time:    Tue Nov  5 23:21:26 2019
Kernel:  SSE2 - 1 threads (24 CPU cores detected)

HINT: Use -nt option to specify number of threads because your CPU has 24 cores!
HINT: -nt AUTO will automatically determine the best number of threads to use.

Reading alignment file Troglosironidae_18S.mafft.fasta ... Fasta format detected
Alignment most likely contains DNA/RNA sequences
WARNING: 1 sites contain only gaps or ambiguous characters.
Alignment has 33 sequences with 1762 columns, 123 distinct patterns
13 parsimony-informative, 48 singleton sites, 1701 constant sites
                               Gap/Ambiguity  Composition  p-value
   1  P_gabonica_IZ132297              0.06%    passed     99.23%
   2  H_tama_IZ134691                  0.06%    passed     98.76%
   3  M_savannahensis_IZ134557         0.96%    passed     99.99%
   4  O_cameroonensis_IZ132315         0.06%    passed     99.67%
   5  T_monteithi_IZ51948              2.38%    passed     99.44%
   6  T_longifossa_IZ65208             0.11%    passed     99.95%
   7  T_oscitatio_IZ72572              0.11%    passed     99.99%
   8  T_pin_IZ133854_1                 0.11%    passed     99.99%
   9  T_pseudojuberthiei_IZ133855_1    0.11%    passed     99.99%
  10  T_pseudojuberthiei_IZ133856      0.11%    passed     99.99%
  11  T_pseudojuberthiei_IZ133857_2    0.11%    passed     99.99%
  12  T_juberthiei_IZ134763m           0.11%    passed     99.99%
  13  T_juberthiei_IZ134763f           0.11%    passed     99.99%
  14  T_cf_platnicki_IZ134766          0.11%    passed     99.99%
  15  T_juberthiei_IZ134767_1          0.11%    passed     99.99%
  16  T_wilsoni_IZ134787               0.23%    passed     99.98%
  17  T_sharmai_IZ151558_1             0.11%    passed     99.99%
  18  T_sharmai_IZ151558_2             0.11%    passed     99.99%
  19  T_dogny_IZ151570_1               0.11%    passed     99.99%
  20  T_dogny_IZ151570_2               0.11%    passed     99.99%
  21  T_pseudojuberthiei_IZ151618_1    0.11%    passed     99.99%
  22  T_pseudojuberthiei_IZ151618_2    0.11%    passed     99.99%
  23  T_urbanus_IZ134780m              3.29%    passed     99.61%
  24  T_pseudojuberthiei_IZ133870      1.08%    passed     99.86%
  25  T_ninqua_IZ134768                0.11%    passed     99.84%
  26  Troglosiro_sp_IZ134782           7.15%    passed     94.15%
  27  T_pin_IZ133875                   0.34%    passed     99.96%
  28  T_urbanus_IZ134780f              1.82%    passed     99.86%
  29  T_aelleni_IZ134764               0.11%    passed     99.85%
  30  T_raveni_IZ134777               33.88%    passed     91.44%
  31  T_sheari_IZ72565                16.63%    passed     93.82%
  32  T_pseudojuberthiei_IZ133870_5   54.77%    passed     81.76%
  33  T_pseudojuberthiei_IZ133859_2   51.59%    passed     94.55%
WARNING: 2 sequences contain more than 50% gaps/ambiguity
****  TOTAL                            5.34%  0 sequences failed composition chi2 test (p-value<5%; df=3)
NOTE: T_pin_IZ133854_1 is identical to T_oscitatio_IZ72572 but kept for subsequent analysis
NOTE: 13 identical sequences (see below) will be ignored for subsequent analysis
NOTE: T_pseudojuberthiei_IZ133855_1 (identical to T_oscitatio_IZ72572) is ignored but added at the end
NOTE: T_pseudojuberthiei_IZ133856 (identical to T_oscitatio_IZ72572) is ignored but added at the end
NOTE: T_pseudojuberthiei_IZ133857_2 (identical to T_oscitatio_IZ72572) is ignored but added at the end
NOTE: T_juberthiei_IZ134763m (identical to T_oscitatio_IZ72572) is ignored but added at the end
NOTE: T_juberthiei_IZ134763f (identical to T_oscitatio_IZ72572) is ignored but added at the end
NOTE: T_cf_platnicki_IZ134766 (identical to T_oscitatio_IZ72572) is ignored but added at the end
NOTE: T_juberthiei_IZ134767_1 (identical to T_oscitatio_IZ72572) is ignored but added at the end
NOTE: T_sharmai_IZ151558_1 (identical to T_oscitatio_IZ72572) is ignored but added at the end
NOTE: T_sharmai_IZ151558_2 (identical to T_oscitatio_IZ72572) is ignored but added at the end
NOTE: T_dogny_IZ151570_1 (identical to T_oscitatio_IZ72572) is ignored but added at the end
NOTE: T_dogny_IZ151570_2 (identical to T_oscitatio_IZ72572) is ignored but added at the end
NOTE: T_pseudojuberthiei_IZ151618_1 (identical to T_oscitatio_IZ72572) is ignored but added at the end
NOTE: T_pseudojuberthiei_IZ151618_2 (identical to T_oscitatio_IZ72572) is ignored but added at the end

For your convenience alignment with unique sequences printed to Troglosironidae_18S.mafft.fasta.uniqueseq.phy


Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.000 seconds
NOTE: ModelFinder requires 1 MB RAM!
ModelFinder will test 286 DNA models (sample size: 1762) ...
 No. Model         -LnL         df  AIC          AICc         BIC
  1  JC            2941.755     37  5957.510     5959.141     6160.056
  2  JC+I          2939.131     38  5954.261     5955.981     6162.281
  3  JC+G4         2939.131     38  5954.262     5955.982     6162.282
  4  JC+I+G4       2939.161     39  5956.321     5958.133     6169.815
  5  JC+R2         2940.645     39  5959.290     5961.101     6172.784
  6  JC+R3         2940.329     41  5962.657     5964.659     6187.100
 14  F81+F         2938.930     40  5957.859     5959.765     6176.827
 15  F81+F+I       2936.345     41  5954.690     5956.692     6179.133
 16  F81+F+G4      2936.346     41  5954.693     5956.695     6179.135
 17  F81+F+I+G4    2936.377     42  5956.754     5958.855     6186.670
 18  F81+F+R2      2937.816     42  5959.633     5961.734     6189.550
 19  F81+F+R3      2937.486     44  5962.972     5965.278     6203.837
 27  K2P           2932.629     38  5941.258     5942.979     6149.278
 28  K2P+I         2929.910     39  5937.821     5939.633     6151.315
 29  K2P+G4        2929.911     39  5937.822     5939.634     6151.316
 30  K2P+I+G4      2929.932     40  5939.865     5941.771     6158.833
 31  K2P+R2        2931.484     40  5942.967     5944.873     6161.936
 32  K2P+R3        2931.123     42  5946.246     5948.347     6176.163
 40  HKY+F         2929.826     41  5941.653     5943.655     6166.095
 41  HKY+F+I       2927.067     42  5938.134     5940.235     6168.050
 42  HKY+F+G4      2927.069     42  5938.137     5940.239     6168.054
 43  HKY+F+I+G4    2927.092     43  5940.183     5942.386     6175.574
 44  HKY+F+R2      2928.665     43  5943.329     5945.532     6178.720
 45  HKY+F+R3      2928.283     45  5946.565     5948.978     6192.904
 53  TNe           2926.592     39  5931.184     5932.996     6144.678
 54  TNe+I         2924.333     40  5928.666     5930.572     6147.634
 55  TNe+G4        2924.340     40  5928.679     5930.585     6147.647
 56  TNe+I+G4      2924.357     41  5930.715     5932.717     6155.157
 57  TNe+R2        2925.509     41  5933.018     5935.020     6157.460
 58  TNe+R3        2925.159     43  5936.317     5938.520     6171.708
 66  TN+F          2922.766     42  5929.532     5931.633     6159.448
 67  TN+F+I        2920.517     43  5927.034     5929.236     6162.424
 68  TN+F+G4       2920.521     43  5927.043     5929.245     6162.433
 69  TN+F+I+G4     2920.541     44  5929.082     5931.388     6169.947
 70  TN+F+R2       2921.676     44  5931.351     5933.658     6172.216
 71  TN+F+R3       2921.314     46  5934.628     5937.150     6186.442
 79  K3P           2932.586     39  5943.172     5944.984     6156.666
 80  K3P+I         2929.863     40  5939.726     5941.631     6158.694
 81  K3P+G4        2929.863     40  5939.725     5941.631     6158.694
 82  K3P+I+G4      2929.885     41  5941.769     5943.772     6166.212
 83  K3P+R2        2931.403     41  5944.805     5946.807     6169.247
 84  K3P+R3        2930.977     43  5947.954     5950.156     6183.344
 92  K3Pu+F        2929.781     42  5943.561     5945.663     6173.478
 93  K3Pu+F+I      2927.017     43  5940.033     5942.236     6175.424
 94  K3Pu+F+G4     2927.018     43  5940.036     5942.239     6175.427
 95  K3Pu+F+I+G4   2927.041     44  5942.082     5944.389     6182.947
 96  K3Pu+F+R2     2928.582     44  5945.163     5947.470     6186.028
 97  K3Pu+F+R3     2928.136     46  5948.272     5950.793     6200.085
105  TPM2+F        2929.684     42  5943.369     5945.470     6173.285
106  TPM2+F+I      2926.890     43  5939.779     5941.982     6175.170
107  TPM2+F+G4     2926.893     43  5939.786     5941.988     6175.177
108  TPM2+F+I+G4   2926.916     44  5941.833     5944.139     6182.698
109  TPM2+F+R2     2928.473     44  5944.946     5947.252     6185.811
110  TPM2+F+R3     2928.006     46  5948.012     5950.534     6199.826
118  TPM2u+F       2929.687     42  5943.374     5945.475     6173.290
119  TPM2u+F+I     2926.895     43  5939.790     5941.992     6175.181
120  TPM2u+F+G4    2926.897     43  5939.794     5941.997     6175.185
121  TPM2u+F+I+G4  2926.920     44  5941.840     5944.146     6182.705
122  TPM2u+F+R2    2928.463     44  5944.927     5947.233     6185.792
123  TPM2u+F+R3    2927.983     46  5947.966     5950.488     6199.780
131  TPM3+F        2929.394     42  5942.788     5944.889     6172.705
132  TPM3+F+I      2926.603     43  5939.206     5941.408     6174.596
133  TPM3+F+G4     2926.606     43  5939.212     5941.414     6174.602
134  TPM3+F+I+G4   2926.622     44  5941.244     5943.551     6182.109
135  TPM3+F+R2     2928.163     44  5944.326     5946.632     6185.191
136  TPM3+F+R3     2927.666     46  5947.332     5949.853     6199.145
144  TPM3u+F       2929.396     42  5942.792     5944.893     6172.709
145  TPM3u+F+I     2926.605     43  5939.210     5941.412     6174.600
146  TPM3u+F+G4    2926.608     43  5939.216     5941.418     6174.607
147  TPM3u+F+I+G4  2926.625     44  5941.249     5943.555     6182.114
148  TPM3u+F+R2    2928.153     44  5944.307     5946.613     6185.172
149  TPM3u+F+R3    2927.642     46  5947.285     5949.806     6199.098
157  TIMe          2926.546     40  5933.091     5934.997     6152.060
158  TIMe+I        2924.280     41  5930.559     5932.562     6155.002
159  TIMe+G4       2924.286     41  5930.573     5932.575     6155.015
160  TIMe+I+G4     2924.305     42  5932.610     5934.711     6162.526
161  TIMe+R2       2925.394     42  5934.787     5936.889     6164.704
162  TIMe+R3       2924.942     44  5937.883     5940.190     6178.748
170  TIM+F         2922.716     43  5931.433     5933.635     6166.823
171  TIM+F+I       2920.461     44  5928.922     5931.228     6169.787
172  TIM+F+G4      2920.468     44  5928.936     5931.242     6169.801
173  TIM+F+I+G4    2920.488     45  5930.976     5933.388     6177.315
174  TIM+F+R2      2921.560     45  5933.119     5935.532     6179.459
175  TIM+F+R3      2921.100     47  5936.200     5938.833     6193.488
183  TIM2e         2926.529     40  5933.058     5934.963     6152.026
184  TIM2e+I       2924.252     41  5930.503     5932.506     6154.946
185  TIM2e+G4      2924.257     41  5930.515     5932.517     6154.957
186  TIM2e+I+G4    2924.276     42  5932.552     5934.654     6162.469
187  TIM2e+R2      2925.360     42  5934.720     5936.821     6164.637
188  TIM2e+R3      2924.888     44  5937.776     5940.082     6178.641
196  TIM2+F        2922.620     43  5931.240     5933.443     6166.631
197  TIM2+F+I      2920.340     44  5928.679     5930.986     6169.544
198  TIM2+F+G4     2920.347     44  5928.693     5931.000     6169.558
199  TIM2+F+I+G4   2920.368     45  5930.736     5933.148     6177.075
200  TIM2+F+R2     2921.444     45  5932.888     5935.300     6179.227
201  TIM2+F+R3     2920.963     47  5935.925     5938.558     6193.213
209  TIM3e         2926.057     40  5932.114     5934.020     6151.082
210  TIM3e+I       2923.763     41  5929.526     5931.528     6153.969
211  TIM3e+G4      2923.768     41  5929.536     5931.539     6153.979
212  TIM3e+I+G4    2923.784     42  5931.567     5933.669     6161.484
213  TIM3e+R2      2924.869     42  5933.739     5935.840     6163.655
214  TIM3e+R3      2924.376     44  5936.751     5939.058     6177.617
222  TIM3+F        2922.344     43  5930.688     5932.891     6166.079
223  TIM3+F+I      2920.068     44  5928.136     5930.442     6169.001
224  TIM3+F+G4     2920.074     44  5928.147     5930.454     6169.012
225  TIM3+F+I+G4   2920.091     45  5930.183     5932.595     6176.522
226  TIM3+F+R2     2921.156     45  5932.312     5934.724     6178.651
227  TIM3+F+R3     2920.657     47  5935.314     5937.947     6192.602
235  TVMe          2931.937     41  5945.874     5947.876     6170.317
236  TVMe+I        2929.157     42  5942.313     5944.414     6172.230
237  TVMe+G4       2929.159     42  5942.318     5944.419     6172.234
238  TVMe+I+G4     2929.175     43  5944.349     5946.552     6179.740
239  TVMe+R2       2930.638     43  5947.276     5949.479     6182.667
240  TVMe+R3       2930.050     45  5950.099     5952.512     6196.439
248  TVM+F         2929.202     44  5946.404     5948.710     6187.269
249  TVM+F+I       2926.376     45  5942.751     5945.164     6189.091
250  TVM+F+G4      2926.377     45  5942.754     5945.166     6189.093
251  TVM+F+I+G4    2926.389     46  5944.778     5947.299     6196.591
252  TVM+F+R2      2927.881     46  5947.761     5950.283     6199.575
253  TVM+F+R3      2927.274     48  5950.547     5953.293     6213.309
261  SYM           2925.940     42  5935.879     5937.980     6165.796
262  SYM+I         2923.622     43  5933.244     5935.447     6168.635
263  SYM+G4        2923.627     43  5933.254     5935.457     6168.645
264  SYM+I+G4      2923.644     44  5935.287     5937.594     6176.152
265  SYM+R2        2924.716     44  5937.432     5939.739     6178.297
266  SYM+R3        2924.184     46  5940.367     5942.888     6192.181
274  GTR+F         2922.187     45  5934.374     5936.787     6180.713
275  GTR+F+I       2919.879     46  5931.758     5934.279     6183.571
276  GTR+F+G4      2919.873     46  5931.745     5934.266     6183.559
277  GTR+F+I+G4    2919.891     47  5933.782     5936.414     6191.070
278  GTR+F+R2      2920.947     47  5935.894     5938.526     6193.181
279  GTR+F+R3      2920.410     49  5938.819     5941.682     6207.056
Akaike Information Criterion:           TN+F+I
Corrected Akaike Information Criterion: TN+F+I
Bayesian Information Criterion:         TNe
Best-fit model: TNe chosen according to BIC

All model information printed to Troglosironidae_18S.mafft.fasta.model.gz
CPU time for ModelFinder: 0.700 seconds (0h:0m:0s)
Wall-clock time for ModelFinder: 0.846 seconds (0h:0m:0s)
Generating 1000 samples for ultrafast bootstrap (seed: 382075)...

NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -2941.782
2. Current log-likelihood: -2937.380
3. Current log-likelihood: -2926.596
Optimal log-likelihood: -2926.592
Rate parameters:  A-C: 1.00000  A-G: 1.38614  A-T: 1.00000  C-G: 1.00000  C-T: 4.64140  G-T: 1.00000
Base frequencies:  A: 0.250  C: 0.250  G: 0.250  T: 0.250
Parameters optimization took 3 rounds (0.008 sec)
Computing ML distances based on estimated model parameters... 0.001 sec
Computing BIONJ tree...
0.024 seconds
Log-likelihood of BIONJ tree: -2932.089
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 0.045 second
Computing log-likelihood of 98 initial trees ... 0.113 seconds
Current best score: -2926.572

Do NNI search on 20 best initial trees
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -2926.566
BETTER TREE FOUND at iteration 2: -2926.562
Iteration 10 / LogL: -2926.569 / Time: 0h:0m:0s
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 11: -2926.246
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 12: -2926.221
BETTER TREE FOUND at iteration 20: -2926.220
Iteration 20 / LogL: -2926.220 / Time: 0h:0m:0s
Finish initializing candidate tree set (20)
Current best tree score: -2926.220 / CPU time: 0.540
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
BETTER TREE FOUND at iteration 27: -2926.220
Iteration 30 / LogL: -2926.220 / Time: 0h:0m:0s (0h:0m:3s left)
Iteration 40 / LogL: -2926.220 / Time: 0h:0m:1s (0h:0m:2s left)
BETTER TREE FOUND at iteration 42: -2926.220
BETTER TREE FOUND at iteration 43: -2926.220
BETTER TREE FOUND at iteration 44: -2926.220
UPDATE BEST LOG-LIKELIHOOD: -2926.220
Iteration 50 / LogL: -2926.220 / Time: 0h:0m:1s (0h:0m:2s left)
Log-likelihood cutoff on original alignment: -2953.698
BETTER TREE FOUND at iteration 54: -2926.216
Iteration 60 / LogL: -2926.220 / Time: 0h:0m:1s (0h:0m:2s left)
BETTER TREE FOUND at iteration 62: -2926.216
BETTER TREE FOUND at iteration 67: -2926.216
Iteration 70 / LogL: -2927.195 / Time: 0h:0m:2s (0h:0m:2s left)
BETTER TREE FOUND at iteration 71: -2926.216
UPDATE BEST LOG-LIKELIHOOD: -2926.216
Iteration 80 / LogL: -2926.216 / Time: 0h:0m:2s (0h:0m:2s left)
Iteration 90 / LogL: -2926.216 / Time: 0h:0m:2s (0h:0m:2s left)
UPDATE BEST LOG-LIKELIHOOD: -2926.216
UPDATE BEST LOG-LIKELIHOOD: -2926.216
BETTER TREE FOUND at iteration 98: -2926.216
Iteration 100 / LogL: -2926.216 / Time: 0h:0m:2s (0h:0m:2s left)
Log-likelihood cutoff on original alignment: -2953.814
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.666
NOTE: UFBoot does not converge, continue at least 100 more iterations
Iteration 110 / LogL: -2926.216 / Time: 0h:0m:3s (0h:0m:2s left)
Iteration 120 / LogL: -2926.216 / Time: 0h:0m:3s (0h:0m:2s left)
Iteration 130 / LogL: -2926.216 / Time: 0h:0m:3s (0h:0m:1s left)
Iteration 140 / LogL: -2926.216 / Time: 0h:0m:3s (0h:0m:1s left)
BETTER TREE FOUND at iteration 146: -2926.216
Iteration 150 / LogL: -2926.216 / Time: 0h:0m:3s (0h:0m:2s left)
Log-likelihood cutoff on original alignment: -2954.037
BETTER TREE FOUND at iteration 151: -2926.216
BETTER TREE FOUND at iteration 157: -2926.216
Iteration 160 / LogL: -2926.216 / Time: 0h:0m:4s (0h:0m:2s left)
Iteration 170 / LogL: -2926.218 / Time: 0h:0m:4s (0h:0m:2s left)
BETTER TREE FOUND at iteration 171: -2926.216
BETTER TREE FOUND at iteration 180: -2926.216
Iteration 180 / LogL: -2926.216 / Time: 0h:0m:4s (0h:0m:2s left)
UPDATE BEST LOG-LIKELIHOOD: -2926.216
Iteration 190 / LogL: -2926.853 / Time: 0h:0m:4s (0h:0m:2s left)
Iteration 200 / LogL: -2926.216 / Time: 0h:0m:5s (0h:0m:2s left)
Log-likelihood cutoff on original alignment: -2954.037
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.957
NOTE: UFBoot does not converge, continue at least 100 more iterations
Iteration 210 / LogL: -2926.216 / Time: 0h:0m:5s (0h:0m:2s left)
UPDATE BEST LOG-LIKELIHOOD: -2926.216
Iteration 220 / LogL: -2926.222 / Time: 0h:0m:5s (0h:0m:2s left)
Iteration 230 / LogL: -2926.219 / Time: 0h:0m:5s (0h:0m:1s left)
Iteration 240 / LogL: -2926.223 / Time: 0h:0m:6s (0h:0m:1s left)
BETTER TREE FOUND at iteration 243: -2926.216
Iteration 250 / LogL: -2926.216 / Time: 0h:0m:6s (0h:0m:2s left)
Log-likelihood cutoff on original alignment: -2953.840
UPDATE BEST LOG-LIKELIHOOD: -2926.216
Iteration 260 / LogL: -2926.216 / Time: 0h:0m:6s (0h:0m:2s left)
BETTER TREE FOUND at iteration 266: -2926.215
BETTER TREE FOUND at iteration 269: -2926.215
Iteration 270 / LogL: -2926.853 / Time: 0h:0m:6s (0h:0m:2s left)
BETTER TREE FOUND at iteration 271: -2926.215
BETTER TREE FOUND at iteration 275: -2926.214
Iteration 280 / LogL: -2926.219 / Time: 0h:0m:7s (0h:0m:2s left)
Iteration 290 / LogL: -2926.555 / Time: 0h:0m:7s (0h:0m:2s left)
Iteration 300 / LogL: -2927.193 / Time: 0h:0m:7s (0h:0m:1s left)
Log-likelihood cutoff on original alignment: -2954.091
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.968
NOTE: UFBoot does not converge, continue at least 100 more iterations
UPDATE BEST LOG-LIKELIHOOD: -2926.214
Iteration 310 / LogL: -2926.215 / Time: 0h:0m:7s (0h:0m:2s left)
BETTER TREE FOUND at iteration 312: -2926.214
Iteration 320 / LogL: -2926.215 / Time: 0h:0m:8s (0h:0m:2s left)
BETTER TREE FOUND at iteration 325: -2926.213
Iteration 330 / LogL: -2926.214 / Time: 0h:0m:8s (0h:0m:2s left)
BETTER TREE FOUND at iteration 335: -2926.213
Iteration 340 / LogL: -2926.213 / Time: 0h:0m:8s (0h:0m:2s left)
BETTER TREE FOUND at iteration 346: -2926.212
UPDATE BEST LOG-LIKELIHOOD: -2926.212
Iteration 350 / LogL: -2926.213 / Time: 0h:0m:9s (0h:0m:2s left)
Log-likelihood cutoff on original alignment: -2953.996
Iteration 360 / LogL: -2926.212 / Time: 0h:0m:9s (0h:0m:2s left)
Iteration 370 / LogL: -2926.213 / Time: 0h:0m:9s (0h:0m:2s left)
Iteration 380 / LogL: -2926.218 / Time: 0h:0m:9s (0h:0m:1s left)
UPDATE BEST LOG-LIKELIHOOD: -2926.212
Iteration 390 / LogL: -2926.221 / Time: 0h:0m:10s (0h:0m:1s left)
Iteration 400 / LogL: -2926.213 / Time: 0h:0m:10s (0h:0m:1s left)
Log-likelihood cutoff on original alignment: -2954.172
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.964
NOTE: UFBoot does not converge, continue at least 100 more iterations
Iteration 410 / LogL: -2926.213 / Time: 0h:0m:10s (0h:0m:2s left)
Iteration 420 / LogL: -2926.561 / Time: 0h:0m:11s (0h:0m:2s left)
Iteration 430 / LogL: -2926.213 / Time: 0h:0m:11s (0h:0m:1s left)
BETTER TREE FOUND at iteration 432: -2926.212
UPDATE BEST LOG-LIKELIHOOD: -2926.212
Iteration 440 / LogL: -2926.212 / Time: 0h:0m:11s (0h:0m:2s left)
Iteration 450 / LogL: -2926.213 / Time: 0h:0m:11s (0h:0m:2s left)
Log-likelihood cutoff on original alignment: -2954.172
Iteration 460 / LogL: -2926.213 / Time: 0h:0m:12s (0h:0m:1s left)
BETTER TREE FOUND at iteration 461: -2926.212
BETTER TREE FOUND at iteration 467: -2926.212
UPDATE BEST LOG-LIKELIHOOD: -2926.212
Iteration 470 / LogL: -2926.213 / Time: 0h:0m:12s (0h:0m:2s left)
BETTER TREE FOUND at iteration 472: -2926.212
BETTER TREE FOUND at iteration 474: -2926.212
BETTER TREE FOUND at iteration 478: -2926.212
Iteration 480 / LogL: -2926.212 / Time: 0h:0m:13s (0h:0m:2s left)
UPDATE BEST LOG-LIKELIHOOD: -2926.212
Iteration 490 / LogL: -2926.212 / Time: 0h:0m:13s (0h:0m:2s left)
BETTER TREE FOUND at iteration 498: -2926.212
Iteration 500 / LogL: -2926.212 / Time: 0h:0m:13s (0h:0m:2s left)
Log-likelihood cutoff on original alignment: -2955.828
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.947
NOTE: UFBoot does not converge, continue at least 100 more iterations
Iteration 510 / LogL: -2926.212 / Time: 0h:0m:14s (0h:0m:2s left)
BETTER TREE FOUND at iteration 511: -2926.212
Iteration 520 / LogL: -2926.212 / Time: 0h:0m:14s (0h:0m:2s left)
BETTER TREE FOUND at iteration 526: -2926.212
Iteration 530 / LogL: -2926.217 / Time: 0h:0m:14s (0h:0m:2s left)
BETTER TREE FOUND at iteration 531: -2926.212
BETTER TREE FOUND at iteration 533: -2926.212
BETTER TREE FOUND at iteration 534: -2926.212
Iteration 540 / LogL: -2926.554 / Time: 0h:0m:15s (0h:0m:2s left)
BETTER TREE FOUND at iteration 544: -2926.212
Iteration 550 / LogL: -2926.212 / Time: 0h:0m:15s (0h:0m:2s left)
Log-likelihood cutoff on original alignment: -2955.828
Iteration 560 / LogL: -2926.212 / Time: 0h:0m:15s (0h:0m:2s left)
BETTER TREE FOUND at iteration 569: -2926.212
Iteration 570 / LogL: -2926.212 / Time: 0h:0m:16s (0h:0m:2s left)
Iteration 580 / LogL: -2926.212 / Time: 0h:0m:16s (0h:0m:2s left)
Iteration 590 / LogL: -2926.212 / Time: 0h:0m:16s (0h:0m:2s left)
Iteration 600 / LogL: -2926.212 / Time: 0h:0m:17s (0h:0m:1s left)
Log-likelihood cutoff on original alignment: -2955.828
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.933
NOTE: UFBoot does not converge, continue at least 100 more iterations
Iteration 610 / LogL: -2926.212 / Time: 0h:0m:17s (0h:0m:2s left)
UPDATE BEST LOG-LIKELIHOOD: -2926.212
Iteration 620 / LogL: -2926.212 / Time: 0h:0m:17s (0h:0m:2s left)
Iteration 630 / LogL: -2926.212 / Time: 0h:0m:18s (0h:0m:2s left)
Iteration 640 / LogL: -2926.327 / Time: 0h:0m:18s (0h:0m:1s left)
UPDATE BEST LOG-LIKELIHOOD: -2926.212
Iteration 650 / LogL: -2926.215 / Time: 0h:0m:18s (0h:0m:1s left)
Log-likelihood cutoff on original alignment: -2955.828
Iteration 660 / LogL: -2926.212 / Time: 0h:0m:19s (0h:0m:1s left)
Iteration 670 / LogL: -2926.212 / Time: 0h:0m:19s (0h:0m:0s left)
Iteration 680 / LogL: -2926.213 / Time: 0h:0m:19s (0h:0m:0s left)
BETTER TREE FOUND at iteration 681: -2926.212
Iteration 690 / LogL: -2926.212 / Time: 0h:0m:20s (0h:0m:2s left)
Iteration 700 / LogL: -2926.212 / Time: 0h:0m:20s (0h:0m:2s left)
Log-likelihood cutoff on original alignment: -2955.828
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.961
NOTE: UFBoot does not converge, continue at least 100 more iterations
Iteration 710 / LogL: -2926.212 / Time: 0h:0m:20s (0h:0m:2s left)
Iteration 720 / LogL: -2926.212 / Time: 0h:0m:21s (0h:0m:2s left)
Iteration 730 / LogL: -2926.554 / Time: 0h:0m:21s (0h:0m:2s left)
UPDATE BEST LOG-LIKELIHOOD: -2926.212
Iteration 740 / LogL: -2926.212 / Time: 0h:0m:21s (0h:0m:1s left)
BETTER TREE FOUND at iteration 744: -2926.212
Iteration 750 / LogL: -2926.276 / Time: 0h:0m:22s (0h:0m:2s left)
Log-likelihood cutoff on original alignment: -2955.004
UPDATE BEST LOG-LIKELIHOOD: -2926.212
Iteration 760 / LogL: -2926.212 / Time: 0h:0m:22s (0h:0m:2s left)
Iteration 770 / LogL: -2926.212 / Time: 0h:0m:23s (0h:0m:2s left)
Iteration 780 / LogL: -2926.212 / Time: 0h:0m:23s (0h:0m:1s left)
Iteration 790 / LogL: -2926.212 / Time: 0h:0m:23s (0h:0m:1s left)
BETTER TREE FOUND at iteration 798: -2926.212
Iteration 800 / LogL: -2926.212 / Time: 0h:0m:24s (0h:0m:2s left)
Log-likelihood cutoff on original alignment: -2955.971
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.963
NOTE: UFBoot does not converge, continue at least 100 more iterations
UPDATE BEST LOG-LIKELIHOOD: -2926.212
Iteration 810 / LogL: -2926.212 / Time: 0h:0m:24s (0h:0m:2s left)
UPDATE BEST LOG-LIKELIHOOD: -2926.212
Iteration 820 / LogL: -2926.212 / Time: 0h:0m:24s (0h:0m:2s left)
Iteration 830 / LogL: -2926.212 / Time: 0h:0m:25s (0h:0m:2s left)
Iteration 840 / LogL: -2926.212 / Time: 0h:0m:25s (0h:0m:1s left)
BETTER TREE FOUND at iteration 843: -2926.212
BETTER TREE FOUND at iteration 849: -2926.212
Iteration 850 / LogL: -2926.554 / Time: 0h:0m:26s (0h:0m:3s left)
Log-likelihood cutoff on original alignment: -2955.004
Iteration 860 / LogL: -2926.215 / Time: 0h:0m:26s (0h:0m:2s left)
Iteration 870 / LogL: -2926.912 / Time: 0h:0m:26s (0h:0m:2s left)
BETTER TREE FOUND at iteration 872: -2926.212
UPDATE BEST LOG-LIKELIHOOD: -2926.212
Iteration 880 / LogL: -2926.212 / Time: 0h:0m:27s (0h:0m:2s left)
Iteration 890 / LogL: -2926.850 / Time: 0h:0m:27s (0h:0m:2s left)
BETTER TREE FOUND at iteration 900: -2926.212
Iteration 900 / LogL: -2926.212 / Time: 0h:0m:28s (0h:0m:3s left)
Log-likelihood cutoff on original alignment: -2955.004
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.973
NOTE: UFBoot does not converge, continue at least 100 more iterations
BETTER TREE FOUND at iteration 903: -2926.212
Iteration 910 / LogL: -2926.329 / Time: 0h:0m:28s (0h:0m:2s left)
Iteration 920 / LogL: -2926.554 / Time: 0h:0m:28s (0h:0m:2s left)
Iteration 930 / LogL: -2926.212 / Time: 0h:0m:29s (0h:0m:2s left)
BETTER TREE FOUND at iteration 933: -2926.211
Iteration 940 / LogL: -2926.215 / Time: 0h:0m:29s (0h:0m:2s left)
Iteration 950 / LogL: -2926.847 / Time: 0h:0m:30s (0h:0m:2s left)
Log-likelihood cutoff on original alignment: -2955.004
BETTER TREE FOUND at iteration 951: -2926.211
UPDATE BEST LOG-LIKELIHOOD: -2926.211
Iteration 960 / LogL: -2926.211 / Time: 0h:0m:30s (0h:0m:2s left)
Iteration 970 / LogL: -2926.212 / Time: 0h:0m:31s (0h:0m:2s left)
BETTER TREE FOUND at iteration 971: -2926.211
Iteration 980 / LogL: -2926.211 / Time: 0h:0m:31s (0h:0m:2s left)
BETTER TREE FOUND at iteration 983: -2926.211
UPDATE BEST LOG-LIKELIHOOD: -2926.211
Iteration 990 / LogL: -2926.211 / Time: 0h:0m:32s (0h:0m:3s left)
Iteration 1000 / LogL: -2926.215 / Time: 0h:0m:32s (0h:0m:2s left)
Log-likelihood cutoff on original alignment: -2955.004
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.972
NOTE: UFBoot does not converge, continue at least 100 more iterations
WARNING: bootstrap analysis did not converge. You should rerun with higher number of iterations (-nm option)
TREE SEARCH COMPLETED AFTER 1001 ITERATIONS / Time: 0h:0m:32s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -2926.211
Optimal log-likelihood: -2926.211
Rate parameters:  A-C: 1.00000  A-G: 1.38336  A-T: 1.00000  C-G: 1.00000  C-T: 4.63052  G-T: 1.00000
Base frequencies:  A: 0.250  C: 0.250  G: 0.250  T: 0.250
Parameters optimization took 1 rounds (0.001 sec)
BEST SCORE FOUND : -2926.211

Testing tree branches by SH-like aLRT with 1000 replicates...
0.221 sec.
Creating bootstrap support values...
Split supports printed to NEXUS file Troglosironidae_18S.mafft.fasta.splits.nex
Total tree length: 0.041

Total number of iterations: 1001
CPU time used for tree search: 29.395 sec (0h:0m:29s)
Wall-clock time used for tree search: 32.404 sec (0h:0m:32s)
Total CPU time used: 29.721 sec (0h:0m:29s)
Total wall-clock time used: 32.892 sec (0h:0m:32s)

Computing bootstrap consensus tree...
Reading input file Troglosironidae_18S.mafft.fasta.splits.nex...
20 taxa and 406 splits.
Consensus tree written to Troglosironidae_18S.mafft.fasta.contree
Reading input trees file Troglosironidae_18S.mafft.fasta.contree
Log-likelihood of consensus tree: -2926.233

Analysis results written to: 
  IQ-TREE report:                Troglosironidae_18S.mafft.fasta.iqtree
  Maximum-likelihood tree:       Troglosironidae_18S.mafft.fasta.treefile
  Likelihood distances:          Troglosironidae_18S.mafft.fasta.mldist

Ultrafast bootstrap approximation results written to:
  Split support values:          Troglosironidae_18S.mafft.fasta.splits.nex
  Consensus tree:                Troglosironidae_18S.mafft.fasta.contree
  Screen log file:               Troglosironidae_18S.mafft.fasta.log

Date and Time: Tue Nov  5 23:22:00 2019
